############################################################################## # MC-shell I/O capture file. # Creation Date and Time: Tue Mar 18 14:16:51 2014 ############################################################################## Hello world from PE 0 Vnm_tstart: starting timer 26 (APBS WALL CLOCK).. NOsh_parseInput: Starting file parsing... NOsh: Parsing READ section NOsh: Storing molecule 0 path piplc_hsp82_bound_to_dmpc_allh41.565.pdb NOsh: Storing molecule 1 path piplc_hsp82_memb41.565.pdb NOsh: Storing molecule 2 path dmpc.pdb NOsh: Done parsing READ section NOsh: Done parsing READ section (nmol=3, ndiel=0, nkappa=0, ncharge=0, npot=0) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (417, 481, 481) NOsh: Done parsing ELEC section (nelec = 1) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (417, 481, 481) NOsh: Done parsing ELEC section (nelec = 2) NOsh: Parsing ELEC section NOsh_parseMG: Parsing parameters for MG calculation NOsh_parseMG: Parsing cgcent... PBEparm_parseToken: trying cgcent... MGparm_parseToken: trying cgcent... NOsh_parseMG: Parsing fgcent... PBEparm_parseToken: trying fgcent... MGparm_parseToken: trying fgcent... NOsh_parseMG: Parsing cglen... PBEparm_parseToken: trying cglen... MGparm_parseToken: trying cglen... NOsh_parseMG: Parsing fglen... PBEparm_parseToken: trying fglen... MGparm_parseToken: trying fglen... NOsh_parseMG: Parsing dime... PBEparm_parseToken: trying dime... MGparm_parseToken: trying dime... NOsh_parseMG: Parsing grid... PBEparm_parseToken: trying grid... MGparm_parseToken: trying grid... NOsh_parseMG: Parsing npbe... PBEparm_parseToken: trying npbe... NOsh: parsed npbe NOsh_parseMG: Parsing bcfl... PBEparm_parseToken: trying bcfl... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing ion... PBEparm_parseToken: trying ion... NOsh_parseMG: Parsing pdie... PBEparm_parseToken: trying pdie... NOsh_parseMG: Parsing sdie... PBEparm_parseToken: trying sdie... NOsh_parseMG: Parsing sdens... PBEparm_parseToken: trying sdens... NOsh_parseMG: Parsing chgm... PBEparm_parseToken: trying chgm... MGparm_parseToken: trying chgm... NOsh_parseMG: Parsing mol... PBEparm_parseToken: trying mol... NOsh_parseMG: Parsing srfm... PBEparm_parseToken: trying srfm... NOsh_parseMG: Parsing srad... PBEparm_parseToken: trying srad... NOsh_parseMG: Parsing swin... PBEparm_parseToken: trying swin... NOsh_parseMG: Parsing temp... PBEparm_parseToken: trying temp... NOsh_parseMG: Parsing gamma... PBEparm_parseToken: trying gamma... MGparm_parseToken: trying gamma... NOsh_parseMG: Parsing calcenergy... PBEparm_parseToken: trying calcenergy... NOsh_parseMG: Parsing calcforce... PBEparm_parseToken: trying calcforce... NOsh_parseMG: Parsing write... PBEparm_parseToken: trying write... NOsh_parseMG: Parsing end... MGparm_check: checking MGparm object of type 1. NOsh: nlev = 4, dime = (417, 481, 481) NOsh: Done parsing ELEC section (nelec = 3) NOsh: Parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing PRINT section NOsh: Done parsing file (got QUIT) Valist_readPDB: Counted 34963 atoms Valist_getStatistics: Max atom coordinate: (48.034, 57.35, 87.852) Valist_getStatistics: Min atom coordinate: (-50.553, -59.867, -27.371) Valist_getStatistics: Molecule center: (-1.2595, -1.2585, 30.2405) Valist_readPDB: Counted 4755 atoms Valist_getStatistics: Max atom coordinate: (27.503, 21.415, 87.852) Valist_getStatistics: Min atom coordinate: (-32.69, -23.18, 31.798) Valist_getStatistics: Molecule center: (-2.5935, -0.8825, 59.825) Valist_readPDB: Counted 30208 atoms Valist_getStatistics: Max atom coordinate: (48.034, 57.35, 28.798) Valist_getStatistics: Min atom coordinate: (-50.553, -59.867, -27.371) Valist_getStatistics: Molecule center: (-1.2595, -1.2585, 0.7135) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.592469, 0.610506, 0.600121 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.35718, 0.348369, 0.344215 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.602868, 0.570623, 0.573575 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 121.975 145.263 174.27 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -124.493 -147.78 -113.788 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 73.0345 82.3505 112.853 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -75.5525 -84.8665 -52.3705 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 73.0345 82.3505 112.853 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -75.5525 -84.8665 -52.3705 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 0 (1) to calculation 1 (2) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.592469, 0.610506, 0.600121 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.35718, 0.348369, 0.344215 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.602868, 0.570623, 0.573575 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 121.975 145.263 174.27 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -124.493 -147.78 -113.788 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 73.0345 82.3505 112.853 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -75.5525 -84.8665 -52.3705 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 73.0345 82.3505 112.853 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -75.5525 -84.8665 -52.3705 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 1 (2) to calculation 3 (4) NOsh_setupCalcMGAUTO(nosh.c, 1589): coarse grid center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO(nosh.c, 1594): fine grid center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO (nosh.c, 1606): Coarse grid spacing = 0.592469, 0.610506, 0.600121 NOsh_setupCalcMGAUTO (nosh.c, 1608): Fine grid spacing = 0.35718, 0.348369, 0.344215 NOsh_setupCalcMGAUTO (nosh.c, 1610): Displacement between fine and coarse grids = 0, 0, 0 NOsh: 2 levels of focusing with 0.602868, 0.570623, 0.573575 reductions NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalcMGAUTO (nosh.c, 1704): starting mesh repositioning. NOsh_setupCalcMGAUTO (nosh.c, 1706): coarse mesh center = -1.259 -1.258 30.241 NOsh_setupCalcMGAUTO (nosh.c, 1711): coarse mesh upper corner = 121.975 145.263 174.27 NOsh_setupCalcMGAUTO (nosh.c, 1716): coarse mesh lower corner = -124.493 -147.78 -113.788 NOsh_setupCalcMGAUTO (nosh.c, 1721): initial fine mesh upper corner = 73.0345 82.3505 112.853 NOsh_setupCalcMGAUTO (nosh.c, 1726): initial fine mesh lower corner = -75.5525 -84.8665 -52.3705 NOsh_setupCalcMGAUTO (nosh.c, 1787): final fine mesh upper corner = 73.0345 82.3505 112.853 NOsh_setupCalcMGAUTO (nosh.c, 1792): final fine mesh lower corner = -75.5525 -84.8665 -52.3705 NOsh_setupMGAUTO: Resetting boundary flags NOsh_setupCalc: Mapping ELEC statement 2 (3) to calculation 5 (6) Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 83.5995 Vpbe_ctor2: solute dimensions = 101.602 x 119.897 x 117.818 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (112.915, 131.545, 129.551) Vclist_setupGrid: Grid lower corner = (-57.7169, -67.0309, -34.5349) Vclist_assignAtoms: Have 12775309 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 417, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 53, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 96477537, nc = 197213 Vpmg_ctor2: PMG chose narr = 110350984, narrc = 13873447 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1368379017, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.933000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.280000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.320000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.039600e+02 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.256981e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.600800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.253768e+06 PMG: contraction number = , 4.253768e+06 NEWTON: attempting damping, relres = 9.029122e-02 NEWTON: attempting damping, relres = 5.423980e-01 NEWTON: damping accepted, relres = 9.029122e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.029122e-02 PMG: contraction number = 9.029122e-02 NEWTON: using errtol_s: 3.843680e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.738400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.086872e+05 PMG: contraction number = , 5.086872e+05 PMG: iteration = 2 PMG: relative residual = 1.076233e-02 PMG: contraction number = 1.191958e-01 NEWTON: using errtol_s: 4.581505e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.477800e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.756080e+04 PMG: contraction number = , 7.756080e+04 PMG: iteration = 3 PMG: relative residual = 1.639976e-03 PMG: contraction number = 1.523810e-01 NEWTON: using errtol_s: 6.981345e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.256400e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.391965e+04 PMG: contraction number = , 1.391965e+04 PMG: iteration = 4 PMG: relative residual = 2.942810e-04 PMG: contraction number = 1.794423e-01 NEWTON: using errtol_s: 1.252749e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.128900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.528430e+03 PMG: contraction number = , 2.528430e+03 PMG: iteration = 5 PMG: relative residual = 5.345645e-05 PMG: contraction number = 1.816510e-01 NEWTON: using errtol_s: 2.275631e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.858200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.265610e+02 PMG: contraction number = , 6.265610e+02 PMG: iteration = 6 PMG: relative residual = 1.324667e-05 PMG: contraction number = 2.478031e-01 NEWTON: using errtol_s: 5.639084e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 6.589200e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.666874e+02 PMG: contraction number = , 2.666874e+02 PMG: iteration = 7 PMG: relative residual = 5.638687e-06 PMG: contraction number = 4.256681e-01 NEWTON: using errtol_s: 2.400378e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 7.316900e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.048925e+02 PMG: contraction number = , 1.048925e+02 PMG: iteration = 8 PMG: relative residual = 2.217628e-06 PMG: contraction number = 3.932881e-01 NEWTON: using errtol_s: 9.440402e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 8.084500e+02 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.604514e+01 PMG: contraction number = , 4.604514e+01 PMG: iteration = 9 PMG: relative residual = 9.735059e-07 PMG: contraction number = 4.389851e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.532700e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.866900e+02 Vpmg_setPart: lower corner = (-124.493, -147.78, -113.788) Vpmg_setPart: upper corner = (121.975, 145.263, 174.27) Vpmg_setPart: actual minima = (-124.492, -147.78, -113.788) Vpmg_setPart: actual maxima = (121.974, 145.263, 174.27) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 6.815048966040E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 9.525902309349E+05 kT Vpmg_energy: dielEnergy = 4.762865893806E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.332000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 83.5995 Vpbe_ctor2: solute dimensions = 101.602 x 119.897 x 117.818 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (112.915, 131.545, 129.551) Vclist_setupGrid: Grid lower corner = (-57.7169, -67.0309, -34.5349) Vclist_assignAtoms: Have 12775309 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 417, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 53, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 96477537, nc = 197213 Vpmg_ctor2: PMG chose narr = 110350984, narrc = 13873447 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1368379017, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -75.5525, -84.8665, -52.3705 VPMG::focusFillBound -- New mesh maxs = 73.0345, 82.3505, 112.853 VPMG::focusFillBound -- Old mesh mins = -124.492, -147.78, -113.788 VPMG::focusFillBound -- Old mesh maxs = 121.974, 145.263, 174.27 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: upper corner = (73.0345, 82.3505, 112.853) Vpmg_setPart: actual minima = (-124.492, -147.78, -113.788) Vpmg_setPart: actual maxima = (121.974, 145.263, 174.27) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-75.5525, -84.8665, -52.3705) VPMG::extEnergy Disj part upper corner = (73.0345, 82.3505, 112.853) VPMG::extEnergy Old lower corner = (-124.492, -147.78, -113.788) VPMG::extEnergy Old upper corner = (121.974, 145.263, 174.27) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000939525 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.00140735 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.268500e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.250000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.474000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.045860e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 4.577754e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.103110e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.834511e+06 PMG: contraction number = , 7.834511e+06 NEWTON: attempting damping, relres = 1.543755e-01 NEWTON: attempting damping, relres = 5.768170e-01 NEWTON: damping accepted, relres = 1.543755e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.543755e-01 PMG: contraction number = 1.543755e-01 NEWTON: using errtol_s: 7.066932e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.212650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.785940e+05 PMG: contraction number = , 9.785940e+05 PMG: iteration = 2 PMG: relative residual = 1.925392e-02 PMG: contraction number = 1.247213e-01 NEWTON: using errtol_s: 8.813972e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.297470e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.434694e+05 PMG: contraction number = , 1.434694e+05 PMG: iteration = 3 PMG: relative residual = 2.822258e-03 PMG: contraction number = 1.465809e-01 NEWTON: using errtol_s: 1.291960e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.373220e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.391449e+04 PMG: contraction number = , 2.391449e+04 PMG: iteration = 4 PMG: relative residual = 4.701709e-04 PMG: contraction number = 1.665939e-01 NEWTON: using errtol_s: 2.152327e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.454830e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.024077e+03 PMG: contraction number = , 4.024077e+03 PMG: iteration = 5 PMG: relative residual = 7.911797e-05 PMG: contraction number = 1.682749e-01 NEWTON: using errtol_s: 3.621827e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.532660e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.946678e+02 PMG: contraction number = , 7.946678e+02 PMG: iteration = 6 PMG: relative residual = 1.562334e-05 PMG: contraction number = 1.974689e-01 NEWTON: using errtol_s: 7.151982e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.610060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.180257e+02 PMG: contraction number = , 3.180257e+02 PMG: iteration = 7 PMG: relative residual = 6.253120e-06 PMG: contraction number = 4.002422e-01 NEWTON: using errtol_s: 2.862525e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.690880e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.527897e+02 PMG: contraction number = , 1.527897e+02 PMG: iteration = 8 PMG: relative residual = 3.003897e-06 PMG: contraction number = 4.803837e-01 NEWTON: using errtol_s: 1.375110e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.768560e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.919118e+01 PMG: contraction number = , 6.919118e+01 PMG: iteration = 9 PMG: relative residual = 1.360381e-06 PMG: contraction number = 4.528722e-01 NEWTON: using errtol_s: 6.227491e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 1.849550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.161056e+01 PMG: contraction number = , 3.161056e+01 PMG: iteration = 10 PMG: relative residual = 6.214741e-07 PMG: contraction number = 4.568382e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.580100e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 8.929400e+02 Vpmg_setPart: lower corner = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: upper corner = (73.0345, 82.3505, 112.853) Vpmg_setPart: actual minima = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: actual maxima = (73.0345, 82.3505, 112.853) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 6.447841985473E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 2.197767740537E+06 kT Vpmg_energy: dielEnergy = 1.098875962681E+06 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.260000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 24.6341) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 417, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 53, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 96477537, nc = 197213 Vpmg_ctor2: PMG chose narr = 110350984, narrc = 13873447 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1368379017, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 3.791000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.210000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.318000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.086060e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 6.865587e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.146960e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.785894e+05 PMG: contraction number = , 6.785894e+05 NEWTON: attempting damping, relres = 8.981640e-02 NEWTON: attempting damping, relres = 5.424065e-01 NEWTON: damping accepted, relres = 8.981640e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 8.981640e-02 PMG: contraction number = 8.981640e-02 NEWTON: using errtol_s: 6.166423e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.269340e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.876331e+04 PMG: contraction number = , 8.876331e+04 PMG: iteration = 2 PMG: relative residual = 1.164316e-02 PMG: contraction number = 1.296329e-01 NEWTON: using errtol_s: 7.993715e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.359990e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.394210e+04 PMG: contraction number = , 1.394210e+04 PMG: iteration = 3 PMG: relative residual = 1.827700e-03 PMG: contraction number = 1.569762e-01 NEWTON: using errtol_s: 1.254823e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.447160e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.436653e+03 PMG: contraction number = , 2.436653e+03 PMG: iteration = 4 PMG: relative residual = 3.194186e-04 PMG: contraction number = 1.747653e-01 NEWTON: using errtol_s: 2.192996e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.527780e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.521095e+02 PMG: contraction number = , 4.521095e+02 PMG: iteration = 5 PMG: relative residual = 5.926669e-05 PMG: contraction number = 1.855456e-01 NEWTON: using errtol_s: 4.069006e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.620770e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 9.911467e+01 PMG: contraction number = , 9.911467e+01 PMG: iteration = 6 PMG: relative residual = 1.299281e-05 PMG: contraction number = 2.192262e-01 NEWTON: using errtol_s: 8.920327e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.710410e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.862062e+01 PMG: contraction number = , 2.862062e+01 PMG: iteration = 7 PMG: relative residual = 3.751861e-06 PMG: contraction number = 2.887644e-01 NEWTON: using errtol_s: 2.575873e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.790900e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.077846e+01 PMG: contraction number = , 1.077846e+01 PMG: iteration = 8 PMG: relative residual = 1.412933e-06 PMG: contraction number = 3.765953e-01 NEWTON: using errtol_s: 9.700617e+00 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 2.883810e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.496075e+00 PMG: contraction number = , 4.496075e+00 PMG: iteration = 9 PMG: relative residual = 5.893862e-07 PMG: contraction number = 4.171365e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.797200e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.123400e+02 Vpmg_setPart: lower corner = (-124.493, -147.78, -113.788) Vpmg_setPart: upper corner = (121.975, 145.263, 174.27) Vpmg_setPart: actual minima = (-124.492, -147.78, -113.788) Vpmg_setPart: actual maxima = (121.974, 145.263, 174.27) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.581741624871E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.380098527211E+05 kT Vpmg_energy: dielEnergy = 6.900189090019E+04 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.345000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 34.4284 Vpbe_ctor2: solute dimensions = 63.151 x 46.7042 x 58.714 Vpbe_ctor2: solute charge = -6.15 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (74.5208, 58.9228, 70.3818) Vclist_setupGrid: Grid lower corner = (-39.8539, -30.3439, 24.6341) Vclist_assignAtoms: Have 7368549 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 417, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 53, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 96477537, nc = 197213 Vpmg_ctor2: PMG chose narr = 110350984, narrc = 13873447 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1368379017, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -75.5525, -84.8665, -52.3705 VPMG::focusFillBound -- New mesh maxs = 73.0345, 82.3505, 112.853 VPMG::focusFillBound -- Old mesh mins = -124.492, -147.78, -113.788 VPMG::focusFillBound -- Old mesh maxs = 121.974, 145.263, 174.27 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: upper corner = (73.0345, 82.3505, 112.853) Vpmg_setPart: actual minima = (-124.492, -147.78, -113.788) Vpmg_setPart: actual maxima = (121.974, 145.263, 174.27) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-75.5525, -84.8665, -52.3705) VPMG::extEnergy Disj part upper corner = (73.0345, 82.3505, 112.853) VPMG::extEnergy Old lower corner = (-124.492, -147.78, -113.788) VPMG::extEnergy Old upper corner = (121.974, 145.263, 174.27) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000159557 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.000225661 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.903000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.430000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.349000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.095170e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 7.465390e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.151600e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.324745e+06 PMG: contraction number = , 1.324745e+06 NEWTON: attempting damping, relres = 1.605159e-01 NEWTON: attempting damping, relres = 5.796890e-01 NEWTON: damping accepted, relres = 1.605159e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.605159e-01 PMG: contraction number = 1.605159e-01 NEWTON: using errtol_s: 1.198314e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.261650e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.707845e+05 PMG: contraction number = , 1.707845e+05 PMG: iteration = 2 PMG: relative residual = 2.059776e-02 PMG: contraction number = 1.283222e-01 NEWTON: using errtol_s: 1.537703e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.341700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.515967e+04 PMG: contraction number = , 2.515967e+04 PMG: iteration = 3 PMG: relative residual = 3.033181e-03 PMG: contraction number = 1.472578e-01 NEWTON: using errtol_s: 2.264388e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.423280e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.062954e+03 PMG: contraction number = , 4.062954e+03 PMG: iteration = 4 PMG: relative residual = 4.898159e-04 PMG: contraction number = 1.614859e-01 NEWTON: using errtol_s: 3.656666e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.502450e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.055628e+02 PMG: contraction number = , 7.055628e+02 PMG: iteration = 5 PMG: relative residual = 8.506026e-05 PMG: contraction number = 1.736576e-01 NEWTON: using errtol_s: 6.350080e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.578190e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.429945e+02 PMG: contraction number = , 1.429945e+02 PMG: iteration = 6 PMG: relative residual = 1.723890e-05 PMG: contraction number = 2.026669e-01 NEWTON: using errtol_s: 1.286951e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.662120e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.401891e+01 PMG: contraction number = , 6.401891e+01 PMG: iteration = 7 PMG: relative residual = 7.718041e-06 PMG: contraction number = 4.477107e-01 NEWTON: using errtol_s: 5.761819e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.749380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.351257e+01 PMG: contraction number = , 3.351257e+01 PMG: iteration = 8 PMG: relative residual = 4.040159e-06 PMG: contraction number = 5.234696e-01 NEWTON: using errtol_s: 3.016137e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.858480e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.357964e+01 PMG: contraction number = , 1.357964e+01 PMG: iteration = 9 PMG: relative residual = 1.637159e-06 PMG: contraction number = 4.052214e-01 NEWTON: using errtol_s: 1.222203e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 3.939740e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.590856e+00 PMG: contraction number = , 6.590856e+00 PMG: iteration = 10 PMG: relative residual = 7.945699e-07 PMG: contraction number = 4.853346e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 8.991500e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.323100e+02 Vpmg_setPart: lower corner = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: upper corner = (73.0345, 82.3505, 112.853) Vpmg_setPart: actual minima = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: actual maxima = (73.0345, 82.3505, 112.853) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 2.510009416492E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 3.329702728756E+05 kT Vpmg_energy: dielEnergy = 1.664822041315E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.347000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 70.6459 Vpbe_ctor2: solute dimensions = 101.602 x 119.897 x 58.461 Vpbe_ctor2: solute charge = 5.27356e-16 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (112.915, 131.545, 70.4968) Vclist_setupGrid: Grid lower corner = (-57.7169, -67.0309, -34.5349) Vclist_assignAtoms: Have 17583198 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 417, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 53, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 96477537, nc = 197213 Vpmg_ctor2: PMG chose narr = 110350984, narrc = 13873447 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1368379017, niwk = 750 Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vpmg_fillco: filling boundary arrays Vpmg_fillco: done filling boundary arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 6.273000e+01 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.350000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.321000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.204870e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.570333e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.260030e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.576309e+06 PMG: contraction number = , 3.576309e+06 NEWTON: attempting damping, relres = 9.040874e-02 NEWTON: attempting damping, relres = 5.424111e-01 NEWTON: damping accepted, relres = 9.040874e-02 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 9.040874e-02 PMG: contraction number = 9.040874e-02 NEWTON: using errtol_s: 3.227893e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.364500e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.198865e+05 PMG: contraction number = , 4.198865e+05 PMG: iteration = 2 PMG: relative residual = 1.059232e-02 PMG: contraction number = 1.171604e-01 NEWTON: using errtol_s: 3.781811e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.443060e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.356244e+04 PMG: contraction number = , 6.356244e+04 PMG: iteration = 3 PMG: relative residual = 1.602524e-03 PMG: contraction number = 1.512911e-01 NEWTON: using errtol_s: 5.721542e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.517700e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.145161e+04 PMG: contraction number = , 1.145161e+04 PMG: iteration = 4 PMG: relative residual = 2.886643e-04 PMG: contraction number = 1.801311e-01 NEWTON: using errtol_s: 1.030628e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.594620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.030286e+03 PMG: contraction number = , 2.030286e+03 PMG: iteration = 5 PMG: relative residual = 5.117948e-05 PMG: contraction number = 1.772976e-01 NEWTON: using errtol_s: 1.827278e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.673370e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 4.863933e+02 PMG: contraction number = , 4.863933e+02 PMG: iteration = 6 PMG: relative residual = 1.226099e-05 PMG: contraction number = 2.395684e-01 NEWTON: using errtol_s: 4.377580e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.753350e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.995348e+02 PMG: contraction number = , 1.995348e+02 PMG: iteration = 7 PMG: relative residual = 5.030059e-06 PMG: contraction number = 4.102491e-01 NEWTON: using errtol_s: 1.795898e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.836140e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 7.787585e+01 PMG: contraction number = , 7.787585e+01 PMG: iteration = 8 PMG: relative residual = 1.963103e-06 PMG: contraction number = 3.902743e-01 NEWTON: using errtol_s: 7.008930e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 4.912610e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.367520e+01 PMG: contraction number = , 3.367520e+01 PMG: iteration = 9 PMG: relative residual = 8.488938e-07 PMG: contraction number = 4.324245e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 7.648900e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 7.980900e+02 Vpmg_setPart: lower corner = (-124.493, -147.78, -113.788) Vpmg_setPart: upper corner = (121.975, 145.263, 174.27) Vpmg_setPart: actual minima = (-124.492, -147.78, -113.788) Vpmg_setPart: actual maxima = (121.974, 145.263, 174.27) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 4.217403623193E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 8.145800139143E+05 kT Vpmg_energy: dielEnergy = 4.072845331708E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.305000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vnm_tstart: starting timer 27 (Setup timer).. Setting up PBE object... Vpbe_ctor2: solute radius = 70.6459 Vpbe_ctor2: solute dimensions = 101.602 x 119.897 x 58.461 Vpbe_ctor2: solute charge = 5.27356e-16 Vpbe_ctor2: bulk ionic strength = 0.1 Vpbe_ctor2: xkappa = 0.102972 Vpbe_ctor2: Debye length = 9.71135 Vpbe_ctor2: zkappa2 = 0.848263 Vpbe_ctor2: zmagic = 7042.98 Vpbe_ctor2: Constructing Vclist with 75 x 75 x 75 table Vclist_ctor2: Using 75 x 75 x 75 hash table Vclist_ctor2: automatic domain setup. Vclist_ctor2: Using 2.77 max radius Vclist_setupGrid: Grid lengths = (112.915, 131.545, 70.4968) Vclist_setupGrid: Grid lower corner = (-57.7169, -67.0309, -34.5349) Vclist_assignAtoms: Have 17583198 atom entries Vacc_storeParms: Surf. density = 10 Vacc_storeParms: Max area = 319.84 Vacc_storeParms: Using 3184-point reference sphere Setting up PDE object... Vpmp_ctor2: Using meth = 1, mgsolv = 0 Setting PDE center to local center... Vpmg_ctor2: PMG chose nx = 417, ny = 481, nz = 481 Vpmg_ctor2: PMG chose nlev = 4 Vpmg_ctor2: PMG chose nxc = 53, nyc = 61, nzc = 61 Vpmg_ctor2: PMG chose nf = 96477537, nc = 197213 Vpmg_ctor2: PMG chose narr = 110350984, narrc = 13873447 Vpmg_ctor2: PMG chose n_rpc = 500, n_iz = 250, n_ipc = 500 Vpmg_ctor2: PMG chose nrwk = 1368379017, niwk = 750 Vpmg_ctor2: Filling boundary with old solution! VPMG::focusFillBound -- New mesh mins = -75.5525, -84.8665, -52.3705 VPMG::focusFillBound -- New mesh maxs = 73.0345, 82.3505, 112.853 VPMG::focusFillBound -- Old mesh mins = -124.492, -147.78, -113.788 VPMG::focusFillBound -- Old mesh maxs = 121.974, 145.263, 174.27 VPMG::extEnergy: energy flag = 1 Vpmg_setPart: lower corner = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: upper corner = (73.0345, 82.3505, 112.853) Vpmg_setPart: actual minima = (-124.492, -147.78, -113.788) Vpmg_setPart: actual maxima = (121.974, 145.263, 174.27) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 VPMG::extEnergy: Finding extEnergy dimensions... VPMG::extEnergy Disj part lower corner = (-75.5525, -84.8665, -52.3705) VPMG::extEnergy Disj part upper corner = (73.0345, 82.3505, 112.853) VPMG::extEnergy Old lower corner = (-124.492, -147.78, -113.788) VPMG::extEnergy Old upper corner = (121.974, 145.263, 174.27) Vpmg_qmEnergy: Calculating nonlinear energy VPMG::extEnergy: extQmEnergy = 0.000771843 kT Vpmg_qfEnergyVolume: Calculating energy VPMG::extEnergy: extQfEnergy = 0 kT VPMG::extEnergy: extDiEnergy = 0.00117656 kT Vpmg_fillco: filling in source term. fillcoCharge: Calling fillcoChargeSpline2... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: done filling coefficient arrays Vnm_tstop: stopping timer 27 (Setup timer). CPU TIME = 1.112400e+02 Vnm_tstart: starting timer 28 (Solver timer).. Vnm_tstart: starting timer 30 (NEWDRIV2: fine problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: fine problem setup). CPU TIME = 5.480000e+00 Vnm_tstart: starting timer 30 (NEWDRIV2: coarse problem setup).. Vnm_tstop: stopping timer 30 (NEWDRIV2: coarse problem setup). CPU TIME = 2.944000e+01 Vnm_tstart: starting timer 30 (NEWDRIV2: solve).. Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.146100e+03 PMG: iteration = 0 PMG: relative residual = 1.000000e+00 PMG: contraction number = 1.000000e+00 NEWTON: damping enabled... NEWTON: using errtol_s: 3.831412e+07 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.202590e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.510955e+06 PMG: contraction number = , 6.510955e+06 NEWTON: attempting damping, relres = 1.531971e-01 NEWTON: attempting damping, relres = 5.762671e-01 NEWTON: damping accepted, relres = 1.531971e-01 NEWTON: damping disabled... PMG: iteration = 1 PMG: relative residual = 1.531971e-01 PMG: contraction number = 1.531971e-01 NEWTON: using errtol_s: 5.869614e+06 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.323200e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 8.075795e+05 PMG: contraction number = , 8.075795e+05 PMG: iteration = 2 PMG: relative residual = 1.898599e-02 PMG: contraction number = 1.239318e-01 NEWTON: using errtol_s: 7.274317e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.405550e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.182257e+05 PMG: contraction number = , 1.182257e+05 PMG: iteration = 3 PMG: relative residual = 2.779053e-03 PMG: contraction number = 1.463739e-01 NEWTON: using errtol_s: 1.064770e+05 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.502050e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.983588e+04 PMG: contraction number = , 1.983588e+04 PMG: iteration = 4 PMG: relative residual = 4.659509e-04 PMG: contraction number = 1.676653e-01 NEWTON: using errtol_s: 1.785250e+04 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.601950e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 3.312482e+03 PMG: contraction number = , 3.312482e+03 PMG: iteration = 5 PMG: relative residual = 7.781461e-05 PMG: contraction number = 1.670017e-01 NEWTON: using errtol_s: 2.981398e+03 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.684620e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 6.484186e+02 PMG: contraction number = , 6.484186e+02 PMG: iteration = 6 PMG: relative residual = 1.523129e-05 PMG: contraction number = 1.957382e-01 NEWTON: using errtol_s: 5.835735e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.769380e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.483838e+02 PMG: contraction number = , 2.483838e+02 PMG: iteration = 7 PMG: relative residual = 5.835209e-06 PMG: contraction number = 3.831067e-01 NEWTON: using errtol_s: 2.235709e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.845720e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 1.197728e+02 PMG: contraction number = , 1.197728e+02 PMG: iteration = 8 PMG: relative residual = 2.813472e-06 PMG: contraction number = 4.821545e-01 NEWTON: using errtol_s: 1.077957e+02 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.917310e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 5.558062e+01 PMG: contraction number = , 5.558062e+01 PMG: iteration = 9 PMG: relative residual = 1.305641e-06 PMG: contraction number = 4.640675e-01 NEWTON: using errtol_s: 5.002448e+01 Vnm_tstop: stopping timer 40 (MG iteration). CPU TIME = 5.989940e+03 PMG: iteration = 0 PMG: relative residual = , 1.000000e+00 PMG: contraction number = , 1.000000e+00 PMG: iteration = 1 PMG: relative residual = , 2.553698e+01 PMG: contraction number = , 2.553698e+01 PMG: iteration = 10 PMG: relative residual = 5.998660e-07 PMG: contraction number = 4.594418e-01 Vnm_tstop: stopping timer 30 (NEWDRIV2: solve). CPU TIME = 9.032600e+02 Vnm_tstop: stopping timer 28 (Solver timer). CPU TIME = 9.427600e+02 Vpmg_setPart: lower corner = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: upper corner = (73.0345, 82.3505, 112.853) Vpmg_setPart: actual minima = (-75.5525, -84.8665, -52.3705) Vpmg_setPart: actual maxima = (73.0345, 82.3505, 112.853) Vpmg_setPart: bflag[FRONT] = 0 Vpmg_setPart: bflag[BACK] = 0 Vpmg_setPart: bflag[LEFT] = 0 Vpmg_setPart: bflag[RIGHT] = 0 Vpmg_setPart: bflag[UP] = 0 Vpmg_setPart: bflag[DOWN] = 0 Vnm_tstart: starting timer 29 (Energy timer).. Vpmg_energy: calculating full PBE energy Vpmg_qmEnergy: Calculating nonlinear energy Vpmg_energy: qmEnergy = 3.927111863532E+00 kT Vpmg_qfEnergyVolume: Calculating energy Vpmg_energy: qfEnergy = 1.864797129135E+06 kT Vpmg_energy: dielEnergy = 9.323936010376E+05 kT Vnm_tstop: stopping timer 29 (Energy timer). CPU TIME = 2.356000e+01 Vnm_tstart: starting timer 30 (Force timer).. Vnm_tstop: stopping timer 30 (Force timer). CPU TIME = 0.000000e+00 Vgrid_writeDX: Opening virtual socket... Vgrid_writeDX: Writing to virtual socket... Vgrid_writeDX: Writing comments for ASC format. printEnergy: Performing global reduction (sum) Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vcom_reduce: Not compiled with MPI, doing simple copy. Vnm_tstop: stopping timer 26 (APBS WALL CLOCK). CPU TIME = 6.164070e+03